[petsc-users] Correlation between da_refine and pg_mg_levels

Thu Mar 30 16:15:07 CDT 2017

Okay I'll give it a shot.

Somewhat unrelated, but I tried running this on Cori's Haswell node (loaded
the module 'petsc/3.7.4-64'). But I get these errors:

[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: Partition in y direction is too fine! 0 1
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016
[0]PETSC ERROR: /global/u1/j/jychang/Icesheet/./ex48 on a
arch-cori-opt64-INTEL-3.7.4-64 named nid00020 by jychang Thu Mar 30
14:04:35 2017
[0]PETSC ERROR: Configure options --known-sizeof-void-p=8
--known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8
--known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-size_t=8
--known-mpi-int64_t=1 --known-has-attribute-aligned=1
--prefix=/global/common/cori/software/petsc/3.7.4-64/hsw/intel
PETSC_ARCH=arch-cori-opt64-INTEL-3.7.4-64 --COPTFLAGS="-mkl -O2 -no-ipo -g
-axMIC-AVX512,CORE-AVX2,AVX" --CXXOPTFLAGS="-mkl -O2 -no-ipo -g
-axMIC-AVX512,CORE-AVX2,AVX" --FOPTFLAGS="-mkl -O2 -no-ipo -g
-axMIC-AVX512,CORE-AVX2,AVX"
--with-hdf5-dir=/opt/cray/pe/hdf5-parallel/1.8.16/INTEL/15.0
--with-hwloc-dir=/global/common/cori/software/hwloc/1.11.4/hsw
--with-scalapack-include=/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/include
--with-scalapack-lib= --LIBS="-mkl
-L/global/common/cori/software/petsc/3.7.4-64/hsw/intel/lib
-I/global/common/cori/software/petsc/3.7.4-64/hsw/intel/include
-L/global/common/cori/software/xz/5.2.2/hsw/lib
-I/global/common/cori/software/xz/5.2.2/hsw/include
-L/global/common/cori/software/zlib/1.2.8/hsw/intel/lib
-I/global/common/cori/software/zlib/1.2.8/hsw/intel/include
-L/global/common/cori/software/libxml2/2.9.4/hsw/lib
-I/global/common/cori/software/libxml2/2.9.4/hsw/include
-L/global/common/cori/software/numactl/2.0.11/hsw/lib
-I/global/common/cori/software/numactl/2.0.11/hsw/include
-L/global/common/cori/software/hwloc/1.11.4/hsw/lib
-I/global/common/cori/software/hwloc/1.11.4/hsw/include
-L/global/common/cori/software/openssl/1.1.0a/hsw/lib
-I/global/common/cori/software/openssl/1.1.0a/hsw/include
-L/global/common/cori/software/subversion/1.9.4/hsw/lib
-I/global/common/cori/software/subversion/1.9.4/hsw/include -lhwloc
-lpciaccess -lxml2 -lz -llzma -Wl,--start-group
/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a
/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_core.a
/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_intel_thread.a
/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a
-Wl,--end-group -lstdc++" --download-parmetis --download-metis --with-ssl=0
--with-batch --known-mpi-shared-libraries=0 --with-clib-autodetect=0
--with-cxxlib-autodetect=0 --with-debugging=0
--with-fortranlib-autodetect=0 --with-mpiexec=srun
--with-shared-libraries=0 --with-x=0 --known-mpi-int64-t=0
--known-bits-per-byte=8 --known-sdot-returns-double=0
--known-snrm2-returns-double=0 --known-level1-dcache-assoc=0
--known-level1-dcache-linesize=32 --known-level1-dcache-size=32768
--known-memcmp-ok=1 --known-mpi-c-double-complex=1
--known-mpi-long-double=1 --known-sizeof-MPI_Comm=4
--known-sizeof-MPI_Fint=4 --known-sizeof-char=1 --known-sizeof-double=8
CC=cc MPICC=cc CXX=CC MPICXX=CC FC=ftn F77=ftn F90=ftn MPIF90=ftn
MPIF77=ftn CFLAGS=-axMIC-AVX512,CORE-AVX2,AVX
CXXFLAGS=-axMIC-AVX512,CORE-AVX2,AVX FFLAGS=-axMIC-AVX512,CORE-AVX2,AVX
CC=cc MPICC=cc CXX=CC MPICXX=CC FC=ftn F77=ftn F90=ftn MPIF90=ftn
MPIF77=ftn CFLAGS=-fPIC FFLAGS=-fPIC LDFLAGS=-fPIE --download-hypre
--with-64-bit-indices
[0]PETSC ERROR: #1 DMSetUp_DA_3D() line 298 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/impls/da/da3.c
[0]PETSC ERROR: #2 DMSetUp_DA() line 27 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/impls/da/dareg.c
[0]PETSC ERROR: #3 DMSetUp() line 744 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/interface/dm.c
[0]PETSC ERROR: #4 DMCoarsen_DA() line 1196 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/impls/da/da.c
[0]PETSC ERROR: #5 DMCoarsen() line 2371 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/interface/dm.c
[0]PETSC ERROR: #6 PCSetUp_MG() line 616 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: #7 PCSetUp() line 968 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #8 KSPSetUp() line 390 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #9 KSPSolve() line 599 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #10 SNESSolve_NEWTONLS() line 230 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #11 SNESSolve() line 4005 in
/global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/snes/interface/snes.c
[0]PETSC ERROR: #12 main() line 1548 in
/global/homes/j/jychang/Icesheet/ex48.c
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -da_refine 4
[0]PETSC ERROR: -ksp_rtol 1e-7
[0]PETSC ERROR: -M 5
[0]PETSC ERROR: -N 5
[0]PETSC ERROR: -P 3
[0]PETSC ERROR: -pc_mg_levels 5
[0]PETSC ERROR: -pc_type mg
[0]PETSC ERROR: -thi_mat_type baij
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
Rank 0 [Thu Mar 30 14:04:35 2017] [c0-0c0s5n0] application called
MPI_Abort(MPI_COMM_WORLD, 63) - process 0
srun: error: nid00020: task 0: Aborted
srun: Terminating job step 4363145.1z

it seems to me the PETSc from this module is not registering the
'-da_refine' entry. This is strange because I have no issue with this on
the latest petsc-dev version, anyone know about this error and/or why it
happens?

On Thu, Mar 30, 2017 at 3:39 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Mar 30, 2017 at 3:38 PM, Justin Chang <jychang48 at gmail.com> wrote:
>
>> Okay, got it. What are the options for setting GAMG as the coarse solver?
>>
>
> -mg_coarse_pc_type gamg I think
>
>
>> On Thu, Mar 30, 2017 at 3:37 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Mar 30, 2017 at 3:04 PM, Justin Chang <jychang48 at gmail.com>
>>> wrote:
>>>
>>>> Yeah based on my experiments it seems setting pc_mg_levels to $DAREFINE
>>>> + 1 has decent performance.
>>>>
>>>> 1) is there ever a case where you'd want $MGLEVELS <= $DAREFINE? In
>>>> some of the PETSc tutorial slides (e.g., http://www.mcs.anl.gov/
>>>> petsc/documentation/tutorials/TutorialCEMRACS2016.pdf on slide
>>>> 203/227) they say to use $MGLEVELS = 4 and $DAREFINE = 5, but when I ran
>>>> this, it was almost twice as slow as if $MGLEVELS >= $DAREFINE
>>>>
>>>
>>> Depending on how big the initial grid is, you may want this. There is a
>>> balance between coarse grid and fine grid work.
>>>
>>>
>>>> 2) So I understand that one cannot refine further than one grid point
>>>> in each direction, but is there any benefit to having $MGLEVELS > $DAREFINE
>>>> by a lot?
>>>>
>>>
>>> Again, it depends on the size of the initial grid.
>>>
>>> On really large problems, you want to use GAMG as the coarse solver,
>>> which will move the problem onto a smaller number of nodes
>>> so that you can coarsen further.
>>>
>>>    Matt
>>>
>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On Thu, Mar 30, 2017 at 2:35 PM, Barry Smith <bsmith at mcs.anl.gov>
>>>> wrote:
>>>>
>>>>>
>>>>>   -da_refine $DAREFINE  determines how large the final problem will be.
>>>>>
>>>>>   By default if you don't supply pc_mg_levels then it uses $DAREFINE +
>>>>> 1 as the number of levels of MG to use; for example -da_refine 1 would
>>>>> result in 2 levels of multigrid.
>>>>>
>>>>>
>>>>> > On Mar 30, 2017, at 2:17 PM, Justin Chang <jychang48 at gmail.com>
>>>>> wrote:
>>>>> >
>>>>> > Hi all,
>>>>> >
>>>>> > Just a general conceptual question: say I am tinkering around with
>>>>> SNES ex48.c and am running the program with these options:
>>>>> >
>>>>> > mpirun -n $NPROCS -pc_type mg -M $XSEED -N $YSEED -P $ZSEED
>>>>> -thi_mat_type baij -da_refine $DAREFINE -pc_mg_levels $MGLEVELS
>>>>> >
>>>>> > I am not too familiar with mg, but it seems to me there is a very
>>>>> strong correlation between $MGLEVELS and $DAREFINE as well as perhaps even
>>>>> the initial coarse grid size (provided by $X/YZSEED).
>>>>> >
>>>>> > Is there a rule of thumb on how these parameters should be? I am
>>>>> guessing it probably is also hardware/architectural dependent?
>>>>> >
>>>>> > Thanks,
>>>>> > Justin
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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